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Table 8 Average speed in GO concept pairs per second (pairs/s) for the evaluation of two representative ontology-based similarity measures based on the Gene Ontology [1, 2] (2020-05-02 version, 44509 nodes)) implemented by state-of-the-art SML [34] library and HESML

From: HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

Similarity measure Measure type SML HESML
Avg. speed
(pairs/s)
Avg. speed
(pairs/s)
Rada [71] Edge-counting 0.077 (20) 3.217 (20)
AncSPL-Rada
(this work)
Edge-counting 140422 \((10^7)\)
Lin-Seco [87, 110]
IC model
IC-based 372140 \((10^7)\) 1063219 \((10^7)\)
  1. Best performing values are shown in bold. The number of random GO concept pairs evaluated to measure each value is shown between parentheses